data_3TZ5 # _model_server_result.job_id KlmNkbO7zxqEnDOL9zj32g _model_server_result.datetime_utc '2024-11-14 16:03:58' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3tz5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":389}' # _entry.id 3TZ5 # _exptl.entry_id 3TZ5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 3TZ5 _cell.length_a 127.703 _cell.length_b 127.703 _cell.length_c 73.871 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TZ5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OD1 ASN 279 A ASN 249 1_555 C MG MG . A MG 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc2 A O VAL 328 A VAL 298 1_555 D K K . A K 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? metalc ? metalc3 A O ASP 330 A ASP 300 1_555 D K K . A K 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.854 ? metalc ? metalc4 A O PHE 333 A PHE 303 1_555 D K K . A K 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? metalc ? metalc5 A O GLY 367 A GLY 337 1_555 D K K . A K 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.058 ? metalc ? metalc6 B O1A ADP . A ADP 389 1_555 C MG MG . A MG 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc7 B O1B ADP . A ADP 389 1_555 C MG MG . A MG 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc8 B O2A ADP . A ADP 389 1_555 D K K . A K 391 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.975 ? metalc ? metalc9 C MG MG . A MG 390 1_555 F O HOH . A HOH 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc10 C MG MG . A MG 390 1_555 F O HOH . A HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc11 C MG MG . A MG 390 1_555 F O HOH . A HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 3TZ5 _atom_sites.fract_transf_matrix[1][1] 0.007831 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007831 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.013537 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 ADP A 1 389 1 ADP ADP . C 3 MG A 1 390 1 MG MG . D 4 K A 1 391 1 K K . E 5 CLT A 1 392 1 CLT CLT . F 6 HOH A 1 393 1 HOH HOH . F 6 HOH A 2 394 2 HOH HOH . F 6 HOH A 3 395 3 HOH HOH . F 6 HOH A 4 396 4 HOH HOH . F 6 HOH A 5 397 5 HOH HOH . F 6 HOH A 6 398 6 HOH HOH . F 6 HOH A 7 399 7 HOH HOH . F 6 HOH A 8 400 8 HOH HOH . F 6 HOH A 9 401 9 HOH HOH . F 6 HOH A 10 402 10 HOH HOH . F 6 HOH A 11 403 11 HOH HOH . F 6 HOH A 12 404 12 HOH HOH . F 6 HOH A 13 405 13 HOH HOH . F 6 HOH A 14 406 14 HOH HOH . F 6 HOH A 15 407 15 HOH HOH . F 6 HOH A 16 408 16 HOH HOH . F 6 HOH A 17 409 17 HOH HOH . F 6 HOH A 18 410 18 HOH HOH . F 6 HOH A 19 411 19 HOH HOH . F 6 HOH A 20 412 20 HOH HOH . F 6 HOH A 21 413 21 HOH HOH . F 6 HOH A 22 414 22 HOH HOH . F 6 HOH A 23 415 23 HOH HOH . F 6 HOH A 24 416 24 HOH HOH . F 6 HOH A 25 417 25 HOH HOH . F 6 HOH A 26 418 26 HOH HOH . F 6 HOH A 27 419 27 HOH HOH . F 6 HOH A 28 420 28 HOH HOH . F 6 HOH A 29 421 29 HOH HOH . F 6 HOH A 30 422 30 HOH HOH . F 6 HOH A 31 423 32 HOH HOH . F 6 HOH A 32 424 33 HOH HOH . F 6 HOH A 33 425 34 HOH HOH . F 6 HOH A 34 426 35 HOH HOH . F 6 HOH A 35 427 36 HOH HOH . F 6 HOH A 36 428 37 HOH HOH . F 6 HOH A 37 429 38 HOH HOH . F 6 HOH A 38 430 39 HOH HOH . F 6 HOH A 39 431 40 HOH HOH . F 6 HOH A 40 432 41 HOH HOH . F 6 HOH A 41 433 42 HOH HOH . F 6 HOH A 42 434 43 HOH HOH . F 6 HOH A 43 435 44 HOH HOH . F 6 HOH A 44 436 45 HOH HOH . F 6 HOH A 45 437 46 HOH HOH . F 6 HOH A 46 438 47 HOH HOH . F 6 HOH A 47 439 48 HOH HOH . F 6 HOH A 48 440 49 HOH HOH . F 6 HOH A 49 441 51 HOH HOH . F 6 HOH A 50 442 52 HOH HOH . F 6 HOH A 51 443 53 HOH HOH . F 6 HOH A 52 444 54 HOH HOH . F 6 HOH A 53 445 55 HOH HOH . F 6 HOH A 54 446 56 HOH HOH . F 6 HOH A 55 447 57 HOH HOH . F 6 HOH A 56 448 58 HOH HOH . F 6 HOH A 57 449 61 HOH HOH . F 6 HOH A 58 450 62 HOH HOH . F 6 HOH A 59 451 63 HOH HOH . F 6 HOH A 60 452 65 HOH HOH . F 6 HOH A 61 453 66 HOH HOH . F 6 HOH A 62 454 67 HOH HOH . F 6 HOH A 63 455 68 HOH HOH . F 6 HOH A 64 456 69 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB ADP . . . B 2 4.894 -32.872 -4.661 1 47.77 ? PB ADP 389 A 1 HETATM 2 O O1B ADP . . . B 2 6.208 -33.416 -4.16 1 40.24 ? O1B ADP 389 A 1 HETATM 3 O O2B ADP . . . B 2 4.947 -32.631 -6.138 1 46.88 ? O2B ADP 389 A 1 HETATM 4 O O3B ADP . . . B 2 3.696 -33.647 -4.148 1 48.82 ? O3B ADP 389 A 1 HETATM 5 P PA ADP . . . B 2 5.664 -30.499 -3.183 1 43.55 ? PA ADP 389 A 1 HETATM 6 O O1A ADP . . . B 2 6.445 -31.34 -2.207 1 40.84 ? O1A ADP 389 A 1 HETATM 7 O O2A ADP . . . B 2 4.937 -29.337 -2.604 1 35.49 ? O2A ADP 389 A 1 HETATM 8 O O3A ADP . . . B 2 4.593 -31.421 -3.986 1 55.09 ? O3A ADP 389 A 1 HETATM 9 O O5' ADP . . . B 2 6.657 -30.007 -4.353 1 41.38 ? O5' ADP 389 A 1 HETATM 10 C C5' ADP . . . B 2 6.161 -29.161 -5.384 1 42.03 ? C5' ADP 389 A 1 HETATM 11 C C4' ADP . . . B 2 7.003 -29.303 -6.627 1 48.07 ? C4' ADP 389 A 1 HETATM 12 O O4' ADP . . . B 2 8.241 -28.616 -6.447 1 42.56 ? O4' ADP 389 A 1 HETATM 13 C C3' ADP . . . B 2 7.37 -30.745 -6.941 1 40.9 ? C3' ADP 389 A 1 HETATM 14 O O3' ADP . . . B 2 6.343 -31.349 -7.721 1 49.67 ? O3' ADP 389 A 1 HETATM 15 C C2' ADP . . . B 2 8.652 -30.565 -7.729 1 53.42 ? C2' ADP 389 A 1 HETATM 16 O O2' ADP . . . B 2 8.369 -30.152 -9.074 1 44.64 ? O2' ADP 389 A 1 HETATM 17 C C1' ADP . . . B 2 9.28 -29.333 -7.112 1 35.08 ? C1' ADP 389 A 1 HETATM 18 N N9 ADP . . . B 2 10.33 -29.626 -6.111 1 40.72 ? N9 ADP 389 A 1 HETATM 19 C C8 ADP . . . B 2 10.16 -29.646 -4.765 1 46.03 ? C8 ADP 389 A 1 HETATM 20 N N7 ADP . . . B 2 11.332 -29.908 -4.131 1 41.78 ? N7 ADP 389 A 1 HETATM 21 C C5 ADP . . . B 2 12.277 -30.047 -5.082 1 35.09 ? C5 ADP 389 A 1 HETATM 22 C C6 ADP . . . B 2 13.726 -30.341 -5.116 1 31.87 ? C6 ADP 389 A 1 HETATM 23 N N6 ADP . . . B 2 14.434 -30.533 -3.974 1 34.19 ? N6 ADP 389 A 1 HETATM 24 N N1 ADP . . . B 2 14.322 -30.41 -6.331 1 42.3 ? N1 ADP 389 A 1 HETATM 25 C C2 ADP . . . B 2 13.648 -30.229 -7.482 1 33.92 ? C2 ADP 389 A 1 HETATM 26 N N3 ADP . . . B 2 12.333 -29.964 -7.529 1 41.36 ? N3 ADP 389 A 1 HETATM 27 C C4 ADP . . . B 2 11.609 -29.862 -6.386 1 37.01 ? C4 ADP 389 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 378 _model_server_stats.encode_time_ms 27 _model_server_stats.element_count 27 #